Rosa Rubicondior: Refuting Creationism - A Denisovan Gene Helped Humans Populate The Americas

Sunday, 24 August 2025

Refuting Creationism - A Denisovan Gene Helped Humans Populate The Americas

The proposed evolutionary history of MUC19.
The Denisovan-like haplotype (in orange) was first introgressed from Denisovans into Neanderthals and then introgressed into modern humans. The introgressed haplotype later experienced positive selection in populations from the Americas. The introgressed MUC19 haplotype is composed of a 742-kb region that contains Neanderthal-specific variants (blue). Embedded within this Neanderthal-like region is a 72-kb region containing a high density of Denisovan-specific variants (orange), and an exonic variable number tandem repeat (VNTR) region (gray). The box below the 742-kb region depicts zooming into the MUC19 VNTR region, in which admixed American individuals carry an elevated number of tandem repeat copies.

Fernando A. Villanea et al. (2025)

Extinct human relatives left a genetic gift that helped people thrive in the Americas | Brown University

Another day; another scientific paper showing the Bible to be wrong — not just slightly wrong, but fundamentally, demonstrably, and irretrievably wrong.

This latest blow comes from researchers at Brown University, who have traced a variant of the gene MUC19, originally identified in the extinct archaic hominins known as Denisovans, and found it alive and well today in modern Latin Americans with Indigenous ancestry. They also detected it in ancient DNA recovered from archaeological sites across both North and South America.

The variant is far too common in modern populations to be a trivial accident. Its persistence screams survival advantage. Natural selection has kept it in play because it helps its carriers thrive in the environments the earliest migrants into the Americas encountered.

What does MUC19 do? It helps build mucus — not glamorous, but life-saving. From the saliva that begins digestion to the mucosal barriers in the gut and respiratory tract that fend off infection, this gene equips its owners with a stronger shield against disease.

And where did it come from? The Denisovans. But it likely reached us by way of Neanderthals, with whom Homo sapiens also interbred. In other words, modern humans are not some isolated “special creation” freshly minted out of clay a few thousand years ago; we are a patchwork of lineages, woven together by repeated episodes of interbreeding over tens of thousands of years.

For creationists, this paper is a nightmare. First, the scientists are explicit: the explanation rests entirely on Evolution and the blind, natural processes that drive it. Second, the mere fact that extinct species like Denisovans and Neanderthals could successfully mate with our ancestors drives a stake through the heart of biblical literalism. Instead of Adam and Eve, what we see is gradual emergence — modern humans arising by incomplete speciation across a broad geographical spread, with genes flowing back and forth whenever populations met again. This pattern repeats itself throughout hominin history, and it unfolds on a timeline that makes the biblical six-thousand-year fantasy look laughably naïve.

The MUC19 Gene

What it is:

MUC19 belongs to the mucin family of genes. Mucins are large, heavily glycosylated proteins that make up mucus — the slimy, protective coating that lines our respiratory, digestive, and reproductive tracts.
Function:

MUC19 helps produce the gel-like consistency of mucus, contributing to:

Lubrication of food in the mouth (via saliva).
Protection of epithelial surfaces from pathogens.
Formation of mucosal barriers that trap microbes and particles before they can cause infection.

Evolutionary origins:

The mucin gene family is ancient, with roots stretching back hundreds of millions of years in vertebrates.
MUC19 itself arose by gene duplication and diversification within this family. Different mucins have been recruited for specialised roles — for example, MUC2 in the gut and MUC5 in the lungs.
The Denisovan variant of MUC19 is one such adaptation, likely honed in Ice Age Eurasia where pathogens and harsh environments placed strong selective pressures on immune defences.

Human inheritance:

Genetic evidence suggests that Homo sapiens acquired this variant of MUC19 through introgression — the flow of genes from Denisovans (probably via Neanderthals) into the modern human gene pool.
The variant persisted at high frequencies in the Americas because it provided a survival advantage against local environmental challenges.

Why it matters:

The story of MUC19 illustrates how evolution works not only through slow accumulation of mutations, but also by horizontal gene transfers from related species. Human biology today is a mosaic assembled from many ancestral sources.

The research team, led by Professor Emilia Huerta-Sánchez of Brown University’s Department of Ecology, Evolution, and Organismal Biology, have published their findings in Science, with further details explained in a Brown University news release by Kevin Stacey.

Another brick out of the crumbling wall of creationist delusion; another win for science.

Extinct human relatives left a genetic gift that helped people thrive in the Americas
A new study found that a gene passed down from extinct archaic humans provided an adaptive advantage for Indigenous people of the Americas and is still common today in people of Indigenous descent.
A new study provides fresh evidence that ancient interbreeding with archaic human species may have provided modern humans with a genetic variant that helped them adapt to new environments as they dispersed across the globe.

The study, published in Science, focused on a gene known as MUC19, which is involved in the production of proteins that form saliva and mucosal barriers in the respiratory and digestive tracts. The researchers show that a variant of that gene derived from Denisovans, an enigmatic species of archaic humans, is present in modern Latin Americans with Indigenous American ancestry, as well as in DNA collected from individuals excavated at archeological sites across North and South America.

The frequency at which the gene appears in modern human populations suggests the gene was under significant natural selection, meaning it provided a survival or reproductive advantage to those who carried it. It’s not clear exactly what that advantage might have been — but given the gene’s involvement in immune processes, it may have helped populations fight off pathogens encountered as they migrated into the Americas thousands of years ago.

From an evolutionary standpoint, this finding shows how ancient interbreeding can have effects that we still see today. From a biological standpoint, we identify a gene that appears to be adaptive, but whose function hasn’t yet been characterized. We hope that leads to additional study of what this gene is actually doing.

Professor Emilia Huerta-Sánchez, senior author.
Department of Ecology, Evolution, and Organismal Biology
Brown University, Providence, RI, USA.

Not much is known about the Denisovans, who lived in Asia between 300,000 and 30,000 years ago, aside from a few small fossils from Denisova cave in Siberia, two jaw bones found in Tibet and Taiwan, and a nearly complete skull from China found this year. A finger fossil from Siberia contained ancient DNA, which has enabled scientists to look for common genes between Denisovans and modern humans. Prior research led by Huerta-Sánchez found that a version of a gene called EPAS1 acquired from Denisovans may have helped Sherpas and other Tibetans to adapt to high altitudes.

For this study, the researchers compared Denisovan DNA with modern genomes collected through the 1,000 Genomes Project, a survey of worldwide genetic variation. The researchers found that the Denisovan-derived MUC19 gene is present in high frequencies in Latino populations who harbor Indigenous American genetic ancestry. The researchers also looked for the gene in the DNA of 23 individuals collected from archeological sites in Alaska, California, Mexico and elsewhere in the Americas. The Denisovan-derived variant was present at high frequency in these ancient individuals as well.

The team used several independent statistical tests to show that the Denisovan MUC19 gene variant rose to unusually high frequencies in ancient Indigenous American populations and present-day people of Indigenous descent, and that the gene sits on an unusually long stretch of archaic DNA — both signs that natural selection had boosted its prevalence. The research also revealed that the gene was likely passed through interbreeding from Denisovans to another archaic population, the Neanderthals, who then interbred with modern humans.

Huerta-Sánchez said the findings demonstrate the importance that interbreeding had in introducing new and potentially useful genetic variation in the human lineage.

Typically, genetic novelty is generated through a very slow process, but these interbreeding events were a sudden way to introduce a lot of new variation.

Professor Emilia Huerta-Sánchez.

In this case, she said, that “new reservoir of genetic variation” appears to have helped modern humans as they migrated into the Americas, perhaps providing a boost to the immune system.

Something about this gene was clearly useful for these populations — and maybe still is or will be in the future.

Professor Emilia Huerta-Sánchez.

She’s hopeful that the recognition of the gene’s importance will spur new research into its function to reveal novel biological mechanisms, especially since it involves coding genetic variants that alter the protein sequence.

Huerta-Sánchez co-authored the study with Fernando Villanea, a former postdoctoral researcher at Brown who is now at University of Colorado, Boulder; David Peede, a graduate student at Brown; and an international team of collaborators.

Publication:
Fernando A. Villanea et al.
The MUC19 gene: An evolutionary history of recurrent introgression and natural selection. Science 389, eadl0882 (2025). DOI: 10.1126/science.adl0882

Structured Abstract

INTRODUCTION
Modern human genomes contain a small number of archaic variants, the legacy of past interbreeding events with Neanderthals and Denisovans. Most of these variants are putatively neutral, but some archaic variants found in modern humans have been targets of positive natural selection and may have been pivotal for adapting to new environments as humans populated the world. American populations encountered a myriad of novel environments, providing the opportunity for natural selection to favor archaic variants in these new environmental contexts. Indigenous and admixed American populations have been understudied in this regard but present great potential for studying the underlying evolutionary processes of local adaptation.

RATIONALE
Previous studies identified the gene MUC19—which codes for a mucin involved in immunity—as a candidate for introgression from Denisovans as well as a candidate for positive natural selection in present-day Indigenous and admixed American populations. Therefore, we sought to confirm and further characterize signatures of both archaic introgression and positive selection at MUC19, with particular interest in modern and ancient American populations.

RESULTS
We identify an archaic haplotype segregating at high frequency in most admixed American populations, and among ancient genomes from 23 ancient Indigenous American individuals who predate admixture with Europeans and Africans. We conclude that the archaic haplotype has undergone positive natural selection in these populations, which is tied to their Indigenous components of ancestry. We also find that modern admixed American individuals exhibit an elevated number of variable number tandem repeats (VNTRs) at MUC19, which codes for the functional domain of the MUC19 protein, where it binds to oligosaccharides to form a glycoprotein, a characteristic of the mucins. Remarkably, we find an association between the number of VNTRs and the number of introgressed haplotypes; individuals harboring introgressed haplotypes tend to have a higher number of VNTRs. In addition to the differences in VNTRs, we find that the archaic MUC19 haplotype contains nine Denisovan-specific, nonsynonymous variants found at high frequencies in American populations. Finally, we observed that the Denisovan-specific variants are contained in a 72-kb region of the MUC19 gene, but that region is embedded in a larger 742-kb region that contains Neanderthal-specific variants. When we studied MUC19 in three high-coverage Neanderthal individuals, we found that the Chagyrskaya and Vindija Neanderthals carry the Denisovan-like haplotype in its heterozygous form. These two Neanderthals also carry another haplotype that is shared with the Altai Neanderthals.

CONCLUSION
Our study identifies several aspects of the gene MUC19 that highlight its importance for studying adaptive introgression: One of the haplotypes that span this gene in modern humans is of archaic origin, and modern humans inherited this haplotype from Neanderthals who likely inherited it from Denisovans. Then, as modern human populations expanded into the Americas, our results suggest that they experienced a massive coding VNTR expansion, which occurred on an archaic haplotype background in MUC19. The functional impact of the variation at this gene may help explain how mainland Indigenous Americans adapted to their environments, which remains underexplored. Our results point to a complex pattern of multiple introgression events, from Denisovans to Neanderthals and Neanderthals to modern humans, which may have later played a distinct role in the evolutionary history of Indigenous American populations.

The proposed evolutionary history of MUC19.
The Denisovan-like haplotype (in orange) was first introgressed from Denisovans into Neanderthals and then introgressed into modern humans. The introgressed haplotype later experienced positive selection in populations from the Americas. The introgressed MUC19 haplotype is composed of a 742-kb region that contains Neanderthal-specific variants (blue). Embedded within this Neanderthal-like region is a 72-kb region containing a high density of Denisovan-specific variants (orange), and an exonic variable number tandem repeat (VNTR) region (gray). The box below the 742-kb region depicts zooming into the MUC19 VNTR region, in which admixed American individuals carry an elevated number of tandem repeat copies.
Fernando A. Villanea et al. (2025)

Abstract
We study the gene MUC19, for which some modern humans carry a Denisovan-like haplotype. MUC19 is a mucin, a glycoprotein that forms gels with various biological functions. We find diagnostic variants for the Denisovan-like MUC19 haplotype at high frequencies in admixed American individuals and at highest frequency in 23 ancient Indigenous American individuals, all pre-dating population admixture with Europeans and Africans. We find that the Denisovan-like MUC19 haplotype is under positive selection and carries a higher copy number of a 30–base-pair variable number tandem repeat, and that copy numbers of this repeat are exceedingly high in admixed American populations. Finally, we find that some Neanderthals carry the Denisovan-like MUC19 haplotype, and that it was likely introgressed into modern human populations through Neanderthal introgression rather than Denisovan introgression.

Fernando A. Villanea et al.
The MUC19 gene: An evolutionary history of recurrent introgression and natural selection. Science 389, eadl0882 (2025). DOI: 10.1126/science.adl0882

© 2025 the American Association for the Advancement of Science.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

So here we have it yet again: a gene that entered the human lineage not by divine fiat, but by the messy, natural processes of interbreeding, survival, and selection. It is hard to imagine a clearer demonstration of how evolution operates in practice — reshaping our genomes, blending lineages, and preserving whatever works in the long struggle against disease and death.

For creationists, this isn’t just inconvenient; it’s catastrophic. Their worldview depends on a myth of humans created fully formed, apart from and above the rest of nature, a few thousand years ago. But the evidence of MUC19 is another reminder that we are not passengers on a separate track. We are part of the same evolutionary story as Neanderthals, Denisovans, and the countless other hominins who walked the Earth before us.

Science doesn’t just explain our origins better than Genesis — it explains them *at all*. The biblical account collapses under the weight of real data, while evolution continues to weave a coherent, testable, and beautifully messy picture of our past. Each discovery like this adds another nail in the coffin of creationism and another stone in the foundation of our true evolutionary heritage.

The Bible’s story may comfort creationists and make them feel important, but the genome tells the truth.

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